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Crystal structure of octaheme nitrite reductase from Trichlorobacter ammonificans in complex with nitrite
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 20 mM NaNO2, 0.1 M Bis-Tris, pH 5.7, 17-20 % PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.44 α = 90 b = 114.44 β = 90 c = 65.23 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 12M 2017-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.96862 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.55 49.6 0.988 0.998 11.4 4.4 69684
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.59 0.788
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.55 49.6 66322 3361 98.76 0.20558 0.20316 0.2048 0.25495 0.2559 RANDOM 25.172
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.63 -0.31 -0.63 2.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.715 r_dihedral_angle_3_deg 16.978 r_dihedral_angle_4_deg 15.65 r_dihedral_angle_1_deg 7.673 r_long_range_B_refined 6.582 r_mcangle_it 4.314 r_scbond_it 4.09 r_mcbond_it 3.444 r_angle_refined_deg 3.421 r_chiral_restr 0.227
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.715 r_dihedral_angle_3_deg 16.978 r_dihedral_angle_4_deg 15.65 r_dihedral_angle_1_deg 7.673 r_long_range_B_refined 6.582 r_mcangle_it 4.314 r_scbond_it 4.09 r_mcbond_it 3.444 r_angle_refined_deg 3.421 r_chiral_restr 0.227 r_gen_planes_refined 0.023 r_bond_refined_d 0.022 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3891 Nucleic Acid Atoms Solvent Atoms 450 Heterogen Atoms 350
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing